Investigators say the bombs, which exploded 12 seconds apart, were designed to deliver the most vicious suffering.
One was housed in a pressure cooker hidden inside a backpack, the FBI said. The device also had fragments that may have included nails, BBs and ball bearings, the agency said.
The second bomb was in a metal container, but it was unclear whether it was in a pressure cooker as well, the FBI said.
Photos obtained by CNN show the remains of a pressure cooker found at the scene, along with a shredded black backpack and what appear to be metal pellets or ball bearings.
They were sent to the FBI's national laboratory in Virginia, where technicians will try to reconstruct the devices.
In the past, the U.S. government has warned federal agencies that terrorists could turn pressure cookers into bombs by packing them with explosives and shrapnel and detonating them with blasting caps.
While the clues moved the investigation forward, it is still unclear whether the attack was an act of domestic or foreign terrorism.
Authorities sifted through thousands of pieces of evidence and a mass of digital photos and video clips. They have pleaded for the public's help in providing additional leads and images.
More than 60 people remained hospitalized Thursday in Boston-area medical centers, seven of them in critical condition, according to hospital officials.
The three dead include:
• Richard, the 8-year-old boy with a gap-tooth grin and bright eyes. He loved to run and play in his yard.
• Campbell, a 29-year-old freckle-faced woman described by her mother as having "a heart of gold."
• Lu, the Chinese graduate student at Boston University who had moved to the city last fall, making friends and soaking up new experiences.
The U.S. State Department has been in contact with her family and the Chinese Foreign Ministry, Secretary of State John Kerry said in a statement released Thursday.
"We stand ready to provide whatever appropriate assistance we can to the family members of foreign nationals in the aftermath of this despicable act of terror," Kerry said.